Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in that rely on the activity of FANCM [Crismani W, et al. (2012) 336:1588-1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) 112:4713-4718], and FIGL1 [Girard C, et al. (2015) 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining and mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.

Meiosis, the specialized cell division that generates gametes, shuffles parental genomes through homologous recombination. It was reported in Drosophila a century ago, that the recombination rate is sensitive to temperature, but how...

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SummaryStructural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined.Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop.We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time.This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.

Meiosis, the basis of sex, evolved through iterative gene duplications. To understand whether subsequent duplications have further enriched the core meiotic "tool-kit," we investigated the fate of meiotic gene duplicates following whole genome duplication (WGD), a common occurrence in eukaryotes. We show that meiotic genes return to a single copy more rapidly than genome-wide average in angiosperms, one of the lineages in which WGD is most vividly exemplified. The rate at which duplicates are lost decreases through time, a tendency that is also observed genome-wide and may thus prove to be a general trend post-WGD. The sharpest decline is observed for the subset of genes mediating meiotic recombination; however, we found no evidence that the presence of these duplicates is counterselected in two recent polyploid crops selected for fertility. We therefore propose that their loss is passive, highlighting how quickly WGDs are resolved in the absence of selective duplicate retention.

Endosymbiotic transfer of DNA and functional genes from the cytoplasmic organelles (mitochondria and chloroplasts) to the nucleus has been a major factor driving the origin of new nuclear genes, a process central to eukaryote evolution. Although organelle DNA transfers very frequently to the nucleus, most is quickly deleted, decays, or is alternatively scrapped. However, a very small proportion of it gives rise, immediately or eventually, to functional genes. To simulate the process of functional transfer, we screened for nuclear activation of a chloroplast reporter gene aadA, which had been transferred from the chloroplast to independent nuclear loci in 16 different plant lines. Cryptic nuclear activity of the chloroplast promoter was revealed, which became conspicuous when present in multiple nuclear copies. We screened ∼50 million cells of each line and retrieved three plants in which aadA showed strong nuclear activation. Activation occurred by acquisition of the CaMV 35S nuclear promoter or by nuclear activation of the native chloroplast promoter. Two fortuitous sites within the 3' UTR of aadA mRNA both promoted polyadenylation without any sequence change. Complete characterization of one nuclear sequence before and after gene transfer demonstrated integration by nonhomologous end joining involving simultaneous insertion of multiple chloroplast DNA fragments. The real-time observation of three different means by which a chloroplast gene can become expressed in the nucleus suggests that the process, though rare, may be more readily achieved than previously envisaged.

Meiotic crossovers shuffle parental genetic information, providing novel combinations 10 of alleles on which natural or artificial selection can act. However, crossover events 11 are relatively rare, typically one to three exchange points per chromosome pair. 12Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis 13 thaliana, that rely on the activity of FANCM 1 , RECQ4 2 and FIGL1 3 , respectively.14 Here, we analyzed recombination in plants where one, two or three of these 15 pathways were disrupted, in both pure line and hybrid contexts. The highest effect 16 was observed when combining recq4 and figl1 mutations, which increased the hybrid 17 genetic map length from 389 to 3037 centiMorgans. This corresponds to an 18 unprecedented 7.8-fold increase in crossover frequency. Disrupting the three 19 pathways do not further increases recombination, suggesting that some upper limit 20 has been reached. The increase in crossovers is not uniform along chromosomes 21 and rises from centromere to telomere. Finally, while in wild type recombination is 22 much higher in male than in female meiosis (490 cM vs 290 cM), female 23 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/159640 doi: bioRxiv preprint first posted online Jul. 6, 2017; 2 recombination is higher than male in recq4 figl1 (3200 cM vs 2720 cM), suggesting Results 66Here we analyzed recombination in single, double and triple mutants for FANCM, 67RECQ4 and FIGL1, in both pure line and hybrid contexts, using two complementary 103We addressed if such a large increase in recombination could reduce the fertility of 104 plants, precluding use of these mutant combinations in breeding programs. In 105. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/159640 doi: bioRxiv preprint first posted online Jul. 6, 2017; 6 hybrids, the number of seeds per fruit was not significantly reduced in any genotype 106 ( Figure 4B). However, a slight defect in pollen viability was observed in single and 107 multi-mutants ( Figure 4D). Further, in pure Col, both reduced seed set and pollen 108 viability defects were detected, and were highest in recq4 figl1 and recq4 figl1 fancm 109 ( Figure 4A, 4C). This suggests that some fertility defects may be associated with 110 increased recombination. However, the fertility defects in the different genotypes are CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/159640 doi: bioRxiv preprint first posted online Jul. 6, 2017; 7 Next, we explored the distribution of COs along the genome (Figure 3 decreases from centromere to telomere ( Figure 3C) may also prevent CO frequency. 164We observed a stro...

Meiosis is a fundamental process in all sexual organisms that ensures fertility and genome stability and creates genetic diversity. For each of these outcomes, the exclusive formation of crossovers between homologous chromosomes is needed. This is more difficult to achieve in polyploid species which have more than 2 sets of chromosomes able to recombine. In this review, we describe how meiosis and meiotic recombination ‘deviate' in polyploid plants compared to diploids, and give an overview of current knowledge on how they are regulated. See also the sister article focusing on animals by Stenberg and Saura in this themed issue.